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Allosteric Modulation of Protein Oligomerization: an Emerging Approach to Drug Design

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Allosteric Modulation of Protein Oligomerization: an Emerging Approach to Drug Design REVIEW ARTICLE published: 24 March 2014 doi: 10.3389/fchem.2014.00009 Allosteric modulation of protein oligomerization: an emerging approach to drug design Ronen Gabizon † and Assaf Friedler* Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel Edited by: Many disease-related proteins are in equilibrium between different oligomeric forms. The Youla S. Tsantrizos, McGill regulation of this equilibrium plays a central role in maintaining the activity of these University, Canada proteins in vitro and in vivo. Modulation of the oligomerization equilibrium of proteins Reviewed by: by molecules that bind preferentially to a specific oligomeric state is emerging as a Lee Fader, Boehringer Ingelheim Pharmaceuticals, Inc., USA potential therapeutic strategy that can be applied to many biological systems such Wolfgang Jahnke, Novartis as cancer and viral infections. The target proteins for such compounds are diverse Institutes for Biomedical Research, in structure and sequence, and may require different approaches for shifting their Switzerland oligomerization equilibrium. The discovery of such oligomerization-modulating compounds *Correspondence: is thus achieved based on existing structural knowledge about the specific target proteins, Assaf Friedler, Institute of Chemistry, The Hebrew University as well as on their interactions with partner proteins or with ligands. In silico design and of Jerusalem, Safra Campus, Givat combinatorial tools such as peptide arrays and phage display are also used for discovering Ram, Jerusalem 91904, Israel compounds that modulate protein oligomerization. The current review highlights some e-mail: [email protected] of the recent developments in the design of compounds aimed at modulating the †Present address: oligomerization equilibrium of proteins, including the “shiftides” approach developed in Ronen Gabizon,California Institute our lab. for Quantitative Biomedical Research (QB3), University of Keywords: protein oligomerization, peptides, HIV-1, drug design, allostery, shiftides California, Berkeley, USA INTRODUCTION of polypeptides under thermal stress conditions. The complex Oligomerization is a common property of proteins and takes undergoes small changes in the inter-subunit interactions when place in all biological systems. It is estimated that at least 35% the temperature increases from 37 to 42–45◦C. This may enable of all proteins in cells are oligomeric (Jones and Thornton, 1996; it to distinguish normal temperatures from stress temperatures Goodsell and Olson, 2000). The properties of protein oligomers (Cabo-Bilbao et al., 2006). Protein oligomerization can also be are highly diverse: Protein oligomers may be homoligomers regulated by the binding of partner proteins (Grossman, 2001; (Wang et al., 1994; Eisenstein and Beckett, 1999; Yun et al., 2007; Fernandez-Fernandez et al., 2005; Marinho-Carvalho et al., 2006; Thulin et al., 2011) or heterooligomers (Fermi et al., 1984; Cramer De Meyts, 2008; Rajagopalan et al., 2008), metal cofactors or small et al., 2001; Unwin et al., 2002; Gomez et al., 2011) and can range molecule allosteric effectors (Kim and Raushel, 2001; Lawrence from dimers (Sapienza et al., 2007) to high order structures such et al., 2008; Selwood et al., 2008; Semenova and Chernoff, 2012). as capsids (Wu and Rossmann, 1993; Nam et al., 2011)andfib- In a notable example, Krojer et al. discovered that the bacterial rils (Craig and Woodhead, 2006; Bedrood et al., 2012). Some HtrA protease exists in an inactive hexameric state, which under- proteins form one specific active oligomeric state. This is the goes an extensive conformational change upon binding to effector case with hemoglobin, which exists in red blood cells as an α2β2 peptides. This change involves the rearrangement of the active site heterotetramer (Fermi et al., 1984), and with the acetylcholine to a catalytically active structure and induces the formation of 12- receptor that is a pentamer (Unwin et al., 2002). Other pro- mer or 24-mer oligomeric states (Krojer et al., 2010). Changes in teins are involved in dynamic oligomerization equilibria between the strength and geometry of interactions between subunits can several states with different activities, and switch between these also be modulated by ATP hydrolysis (Zhang et al., 2010). states as part of regulating their normal function. For exam- Since oligomerization is very common and is crucial for pro- ple, the enzyme carbamoyl phosphate synthase (CPS) exists in tein activity, modulating this process is a highly promising ther- equilibrium between inactive dimers and active tetramers. The apeutic strategy that can be applied to many different diseases equilibrium is regulated by allosteric inhibitors that stabilize the involving oligomeric proteins (Hayouka et al., 2007; Lawrence dimer and allosteric activators that stabilize the tetramer (Kim et al., 2008; Christ et al., 2012; Gabizon et al., 2012). Several com- and Raushel, 2001; Mora et al., 2002). In many cases, the dynamic pounds that are already in clinical use were later discovered to act assembly and disassembly of oligomers plays a central role in reg- via modulation of protein oligomerization. A well-known exam- ulating the activity of a protein, as in the case of actin (Ono, 2007), ple is that of the anti-cancer drug Taxol, which was discovered in which induces cell motility by this mechanism. the stem bark of the pacific yew during the screening of plant- Correct protein oligomerization is critical for its function derived compounds for cytotoxic activity (Wani et al., 1971). It and is therefore tightly regulated by various factors. For exam- was later discovered that Taxol binds to β-tubulin (Löwe et al., ple, the GroEL-GroES chaperonin complex assists in the folding 2001) and allosterically inhibits the assembly and disassembly www.frontiersin.org March 2014 | Volume 2 | Article 9 | 1 Gabizon and Friedler Allosteric modulation of protein oligomerization dynamics of microtubules (Jordan et al., 1993; Derry et al., 1995), thus interfering with mitosis and inhibiting the division of cancer cells. Many compounds that modulate protein oligomerization are still being discovered indirectly by screening methods that do not target protein oligomerization. However, a growing num- ber of studies aim to discover molecules that directly target the oligomerization of a well characterized protein. The understand- ing of oligomeric protein structures and how they are regulated significantly progressed in recent years. Structures determined by NMR and X-ray crystallography enable detailed character- ization of the oligomerization interfaces and the interactions that stabilize the oligomers (see for example Fermi et al., 1984; Jeffrey et al., 1995; Lange-Savage et al., 1997; Luger et al., 1997; Walters et al., 1997; Whitson et al., 2005; Sharma et al., 2010). Methods for precise determination of the oligomeric states of a protein and their relative populations, such as size exclusion chro- matography (SEC) (Mateu and Fersht, 1998; Gotte et al., 2012; Yu et al., 2013), analytical ultracentrifugation (AUC) (Weinberg et al., 2004a; Murugan and Hung, 2012; Szymanski et al., 2013) and single molecule methods (Groulx et al., 2011; Paredes et al., FIGURE 1 | Schematic illustrations of mechanisms of modulation of 2012; Calebiro et al., 2013), improve our understanding of the protein oligomerization. (A) Direct blocking of oligomerization interfaces; thermodynamics and kinetics of oligomerization processes. Based (B) Binding to or near the oligomerization interface and stabilizing it; (C) on this knowledge, molecules that shift the oligomerization equi- Binding to several monomers simultaneously; (D) Morpheein mechanism librium of target proteins are being developed using techniques (Jaffe, 2005). The conformations determine the stoichiometry of the full ranging from de novo design to combinatorial screening. This oligomer. In this example, a ligand binds the monomer and stabilizes the conformation that promotes formation of a different oligomer. review will cover the latest developments in this field and their application to various disease-related proteins. The compounds discussed in this study are summarized in table S1. between active octamers and inactive hexamers. The transition between the two states requires dissociation into dimers followed MECHANISMS OF MODULATING THE OLIGOMERIZATION by a conformational change in the dimer and reassociation. This EQUILIBRIUM OF PROTEINS process can be modulated by allosteric effectors, such as mag- Modulation of protein oligomerization can take place by various nesium, which specifically stabilizes the octamer (Jaffe, 2005). mechanisms. In the simplest mechanism, inhibition of oligomer- Lawrence et al. used in silico screening to develop a compound ization can be achieved by molecules that bind directly to the that inhibits pea PGBS by binding specifically to the inactive hex- oligomerization interface and competitively block it (He et al., amer (Lawrence et al., 2008), thus proving the feasibility of mod- 2005), thus preventing oligomerization (Figure 1A). These com- ulating the activity of proteins by shifting their oligomerization petitive oligomerization inhibitors do not act by stabilizing a equilibrium. Many proteins exhibit characteristics indicating that specific oligomeric state and are thus outside the scope of this their oligomerization dynamics follow the morpheein mechanism review. Alternatively, molecules may stabilize a specific oligomer
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